Just found out that you're back, incredible news! Can't wait to see what you do with these fanedits.
My personal hat in the ring would be to keep Phobos and Last Supper because they give us some much needed time with these characters - Phobos is a great post-title card introduction to the movie. I love the ideas of using Meet Walter for the opening and moving The Crossing to the flashback, I think those are brilliant ideas! Axing the flare scene and the crew messages does seem like the right call, wonderful as the crew messages are - they do feel very wink-nudgey. Maybe a new scene could be created by cutting them together to give the most important information - cryosleep, colonisation, et cetera - I'm feeling inspired to give it a go, though its inclusion is of course entirely up to you!
All in all I'm just super excited to see what you do with these cuts - the Chaos Editions are my favourite ways to experience the prequel movies, and the idea of seeing them improved by things such as moving the Crossing and adding Meet Walter makes me so very happy. Thank you so much for your work and enthusiasm, I can't wait!
Much love <3